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- PDB-5v5x: Protocadherin gammaB7 EC3-6 cis-dimer structure -

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Basic information

Entry
Database: PDB / ID: 5v5x
TitleProtocadherin gammaB7 EC3-6 cis-dimer structure
ComponentsMCG133388, isoform CRA_y
KeywordsCELL ADHESION
Function / homology
Function and homology information


homophilic cell adhesion via plasma membrane adhesion molecules / cell adhesion / calcium ion binding / membrane / plasma membrane
Similarity search - Function
Cadherin, C-terminal catenin-binding domain / Cadherin C-terminal cytoplasmic tail, catenin-binding region / Cadherin, cytoplasmic C-terminal domain / Cadherin cytoplasmic C-terminal / Cadherin, N-terminal / Cadherin-like / Cadherin conserved site / Cadherin domain signature. / Cadherin repeats. / Cadherin domain ...Cadherin, C-terminal catenin-binding domain / Cadherin C-terminal cytoplasmic tail, catenin-binding region / Cadherin, cytoplasmic C-terminal domain / Cadherin cytoplasmic C-terminal / Cadherin, N-terminal / Cadherin-like / Cadherin conserved site / Cadherin domain signature. / Cadherin repeats. / Cadherin domain / Cadherins domain profile. / Cadherin-like / Cadherin-like superfamily
Similarity search - Domain/homology
alpha-D-mannopyranose / Protocadherin gamma B7
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.5 Å
AuthorsGoodman, K.M. / Mannepalli, S. / Bahna, F. / Honig, B. / Shapiro, L.
Funding support United States, 5items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM103403 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM107571 United States
National Institutes of Health/National Institute of Mental Health (NIH/NIMH)MH114817 United States
National Institutes of Health/Office of the DirectorOD012351 United States
National Institutes of Health/Office of the DirectorOD021764 United States
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2017
Title: Protocadherin cis-dimer architecture and recognition unit diversity.
Authors: Goodman, K.M. / Rubinstein, R. / Dan, H. / Bahna, F. / Mannepalli, S. / Ahlsen, G. / Aye Thu, C. / Sampogna, R.V. / Maniatis, T. / Honig, B. / Shapiro, L.
History
DepositionMar 15, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 1, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2017Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.pdbx_database_id_DOI ..._citation.journal_abbrev / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Nov 22, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / struct_asym / struct_conn / struct_conn_type / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _atom_site_anisotrop.id / _atom_site_anisotrop.pdbx_label_asym_id / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn_type.id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Mar 23, 2022Group: Author supporting evidence / Database references ...Author supporting evidence / Database references / Derived calculations / Structure summary
Category: chem_comp / database_2 ...chem_comp / database_2 / pdbx_audit_support / struct_conn
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag
Revision 2.2Oct 4, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: MCG133388, isoform CRA_y
B: MCG133388, isoform CRA_y
C: MCG133388, isoform CRA_y
D: MCG133388, isoform CRA_y
hetero molecules


Theoretical massNumber of molelcules
Total (without water)201,01772
Polymers192,4164
Non-polymers8,60068
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: equilibrium centrifugation, Analytical ultracentrifugation was used to determine the molecule is dimeric.
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area17590 Å2
ΔGint-66 kcal/mol
Surface area89060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.242, 91.762, 452.991
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein / Non-polymers , 2 types, 40 molecules ABCD

#1: Protein
MCG133388, isoform CRA_y / Protocadherin gamma B7 / Protocadherin gamma subfamily B / 7


Mass: 48104.117 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: Extracellular cadherin domains 3-6 with C-terminal octahistidine tag.
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Pcdhgb7, mCG_133388 / Cell line (production host): HEK293F / Production host: Homo sapiens (human) / References: UniProt: Q91XX3
#6: Chemical...
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 36 / Source method: obtained synthetically / Formula: Ca

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Sugars , 6 types, 32 molecules

#2: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 570.542 Da / Num. of mol.: 1 / Source method: obtained synthetically
DescriptorTypeProgram
DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5]/1-1-2/a4-b1_a6-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}[(6+1)][a-L-Fucp]{}}}LINUCSPDB-CARE
#3: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 1 / Source method: obtained synthetically
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#4: Polysaccharide beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 586.542 Da / Num. of mol.: 1 / Source method: obtained synthetically
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}}LINUCSPDB-CARE
#5: Polysaccharide alpha-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 367.349 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
LFucpa1-6DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5]/1-2/a6-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(6+1)][a-L-Fucp]{}}}LINUCSPDB-CARE
#7: Sugar...
ChemComp-MAN / alpha-D-mannopyranose / alpha-D-mannose / D-mannose / mannose


Type: D-saccharide, alpha linking / Mass: 180.156 Da / Num. of mol.: 24 / Source method: obtained synthetically / Formula: C6H12O6
IdentifierTypeProgram
DManpaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-D-mannopyranoseCOMMON NAMEGMML 1.0
a-D-ManpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
ManSNFG CARBOHYDRATE SYMBOLGMML 1.0
#8: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.69 Å3/Da / Density % sol: 66.63 %
Crystal growTemperature: 295 K / Method: batch mode / pH: 7.5
Details: 20% ethylene glycol, 10% PEG8000, 10% Morpheus amino acids additive (Molecular Dimensions), and 0.1M Morpheus Buffer System 2 (HEPES/MOPS buffer, Molecular Dimensions) pH 7.5.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9791 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Oct 21, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 3.5→20 Å / Num. obs: 36143 / % possible obs: 98.02 % / Redundancy: 3.2 % / Biso Wilson estimate: 75.62 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.161 / Net I/σ(I): 6.8

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5SZR

5szr


Resolution: 3.5→19.962 Å / SU ML: 0.43 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.91
RfactorNum. reflection% reflection
Rfree0.2567 1781 4.93 %
Rwork0.2079 --
obs0.2103 36143 98.02 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 3.5→19.962 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12611 0 485 0 13096
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00313333
X-RAY DIFFRACTIONf_angle_d0.55318271
X-RAY DIFFRACTIONf_dihedral_angle_d13.5988131
X-RAY DIFFRACTIONf_chiral_restr0.0422246
X-RAY DIFFRACTIONf_plane_restr0.0032371
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.5-3.59410.41170.31972659X-RAY DIFFRACTION99
3.5941-3.69920.37111470.27662580X-RAY DIFFRACTION99
3.6992-3.81780.29611190.2542658X-RAY DIFFRACTION98
3.8178-3.95330.27911510.2422577X-RAY DIFFRACTION99
3.9533-4.11020.27311260.22092651X-RAY DIFFRACTION99
4.1102-4.29550.30411500.20362630X-RAY DIFFRACTION99
4.2955-4.51950.20851460.18732631X-RAY DIFFRACTION99
4.5195-4.7990.21941350.17472625X-RAY DIFFRACTION98
4.799-5.16360.21891560.16992619X-RAY DIFFRACTION98
5.1636-5.67240.24161440.17652682X-RAY DIFFRACTION98
5.6724-6.46860.25261270.20682644X-RAY DIFFRACTION98
6.4686-8.05950.29391330.22212661X-RAY DIFFRACTION96
8.0595-19.96180.19551300.18082745X-RAY DIFFRACTION94
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
14.4625-0.0767-0.75592.26851.88285.2855-0.2429-0.3106-0.1710.62840.31440.0089-0.17790.0783-0.10670.97520.03460.07080.29140.0220.35226.25811.3205362.3558
22.1758-0.33410.09453.06640.6744.42040.42010.3058-0.0376-0.11870.0231-0.0727-0.84590.3884-0.40170.724-0.04210.20570.359-0.03080.342718.58638.0264315.1818
31.0013-1.2619-1.87981.62942.40246.0662-0.22240.9391-0.18-0.4543-0.1157-0.04760.0683-0.74440.22271.045-0.30010.32731.2483-0.08210.510731.3414-4.6155267.4939
41.6435-0.3663-2.21630.40410.41142.8382-0.23290.6219-0.3311-0.5208-0.0523-0.1161.0778-0.05540.3441.20320.10990.30681.6944-0.04020.562958.3535-12.0649232.1168
53.4851-0.2635-0.00663.37541.06390.3415-0.22580.6498-0.0309-0.68120.1409-0.03980.94070.0047-0.04961.1874-0.04630.13880.4764-0.1450.419414.091-13.9415307.4528
63.9267-1.1533-2.50693.43792.65192.9938-0.0199-0.2808-0.2209-0.0213-0.1327-0.04031.085-0.10470.14960.6060.0254-0.02220.36250.00790.3339.6148-12.4399353.5418
70.35460.1725-1.20011.44320.76688.1472-0.4043-0.82460.37970.12590.0106-0.0491-0.2033-0.95180.26030.85490.3404-0.03681.1475-0.06320.40055.09180.3892403.0296
80.29520.03730.31660.962-0.22930.34990.0969-0.8573-0.10781.64380.0221-0.1732-0.01380.2309-0.09381.37280.427-0.04012.5977-0.04470.547816.45931.9664446.5874
94.21930.27821.15163.6547-0.79310.89840.22240.77080.1012-0.37070.2631-0.174-0.29580.1707-0.26431.2536-0.0410.14180.40080.15630.390366.355311.4866304.1364
104.28131.6086-6.03831.1739-2.02738.6806-0.2241-0.95-0.11460.24760.107-0.0785-0.78640.01350.03651.26130.34180.26991.08660.10510.527637.696-4.121396.1336
110.76240.194-0.86770.271-0.38621.9811-0.265-0.8094-0.10630.19090.16120.17270.5877-0.61220.3311.0460.34910.32362.27750.46060.3410.3706-13.5792431.2916
124.1999-0.35621.23582.4676-0.83087.2028-0.0423-0.5062-0.07360.64830.30260.3143-0.07440.0621-0.28090.9701-0.07870.15140.34270.03210.408953.8087-13.6228358.0423
133.39230.1973-2.77321.9329-0.31322.28120.06330.31730.239-0.25560.13790.14470.815-0.4926-0.06460.8466-0.0864-0.0230.32090.03090.243259.5878-10.398309.9382
141.2829-0.59191.70131.9124-1.54472.63210.10820.92510.0003-0.5609-0.1683-0.09650.04020.68080.07010.92-0.0428-0.03151.14420.0190.423663.55681.7493260.3637
150.32020.040.83450.8728-0.52893.9317-0.1580.787-0.1144-0.84940.0763-0.0143-0.5738-0.12180.03450.97880.22350.03982.2269-0.06020.398351.78113.9578216.3584
160.83780.3194-0.50541.5524-2.04583.9270.48-0.19670.2370.51430.06760.162-1.67380.09-0.47021.43510.0080.2880.48980.03480.529452.661510.0302348.9889
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 209:310 )A209 - 310
2X-RAY DIFFRACTION2( CHAIN A AND RESID 311:415 )A311 - 415
3X-RAY DIFFRACTION3( CHAIN A AND RESID 416:525 )A416 - 525
4X-RAY DIFFRACTION4( CHAIN A AND RESID 526:632 )A526 - 632
5X-RAY DIFFRACTION5( CHAIN B AND RESID 210:310 )B210 - 310
6X-RAY DIFFRACTION6( CHAIN B AND RESID 311:415 )B311 - 415
7X-RAY DIFFRACTION7( CHAIN B AND RESID 416:525 )B416 - 525
8X-RAY DIFFRACTION8( CHAIN B AND RESID 526:632 )B526 - 632
9X-RAY DIFFRACTION9( CHAIN C AND RESID 210:310 )C210 - 310
10X-RAY DIFFRACTION10( CHAIN C AND RESID 416:525 )C416 - 525
11X-RAY DIFFRACTION11( CHAIN C AND RESID 526:632 )C526 - 632
12X-RAY DIFFRACTION12( CHAIN D AND RESID 208:310 )D208 - 310
13X-RAY DIFFRACTION13( CHAIN D AND RESID 311:415 )D311 - 415
14X-RAY DIFFRACTION14( CHAIN D AND RESID 416:525 )D416 - 525
15X-RAY DIFFRACTION15( CHAIN D AND RESID 526:634 )D526 - 634
16X-RAY DIFFRACTION16( CHAIN C AND RESID 311:415 )C311 - 415

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